Contacts of the helix formed by residues 37 - 42 (chain C) in PDB entry 6EKK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A HIS* 4.0 20.6 - - - -
235A LEU* 3.6 31.0 - - + -
238A TYR* 3.6 19.7 - + - +
33C PHE* 3.5 35.4 - + - -
35C GLY 4.6 2.9 - - - -
36C SER* 1.3 72.3 - - - +
38C ILE* 1.3 64.5 - - - +
39C THR 3.2 2.5 - - - -
40C THR* 2.9 36.0 + - + -
41C ILE* 2.9 20.4 + - + -
42C GLY 3.4 0.3 + - - -
43C VAL 3.2 17.9 - - - +
44C ASP* 2.8 13.8 + - - +
203C EDO 3.8 19.7 - - - -
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR 3.5 3.3 - - - +
77A ASP 4.2 0.5 - - - +
78A ILE* 4.6 13.0 - - + -
22C SER* 6.1 3.4 - - - -
36C SER* 3.2 17.3 + - - +
37C TYR* 1.3 76.8 - - - +
39C THR* 1.3 70.7 + - + +
42C GLY* 3.0 25.1 + - - -
43C VAL* 3.5 5.1 + - - +
44C ASP* 3.8 12.8 - - + +
63C ASP* 3.8 26.0 - - - +
64C THR* 3.5 35.7 - - - +
65C ALA* 3.7 19.8 - - + +
204C GDP 6.1 0.4 - - - +
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 5.7 0.3 - - - +
76A THR 3.0 12.3 - - - -
77A ASP* 4.3 3.1 - - + +
78A ILE* 4.0 34.5 - - + +
83A ARG* 2.8 26.3 + - - -
36C SER 4.8 5.4 + - - -
37C TYR 3.2 0.6 - - - -
38C ILE* 1.3 82.6 - - + +
40C THR* 1.3 60.4 + - - +
203C EDO 5.7 0.7 + - - -
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Residues in contact with THR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 4.3 11.9 + - - +
53A PHE* 3.8 31.9 - - + -
75A LEU* 3.2 22.0 - - + +
76A THR 3.0 19.2 + - - -
83A ARG* 4.8 0.2 - - - +
235A LEU* 4.6 1.1 - - + -
36C SER 4.6 0.3 + - - -
37C TYR* 2.9 28.5 + - + -
39C THR* 1.3 83.7 + - - +
41C ILE* 1.3 64.5 + - + +
42C GLY 3.6 0.4 - - - -
203C EDO 3.7 22.7 + - - -
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.7 27.1 - - + -
74A VAL 5.0 3.6 - - - +
76A THR* 3.7 13.6 + - - -
226A VAL* 4.4 4.3 - - - +
227A TYR 4.7 2.8 + - - +
228A ILE* 3.6 42.3 - - + +
231A LEU* 4.5 1.8 - - + -
235A LEU* 4.1 16.4 - - + -
238A TYR* 3.7 39.5 - - + -
37C TYR* 2.9 17.6 + - + +
40C THR* 1.3 79.1 - - - +
42C GLY* 1.3 62.1 + - - +
43C VAL* 3.2 24.8 + - + +
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 5.8 0.9 - - - -
76A THR* 3.6 22.3 - - - -
80A SER* 5.5 0.3 + - - -
226A VAL* 5.0 2.6 - - - +
38C ILE* 3.0 24.3 + - - -
41C ILE* 1.3 77.9 - - - +
43C VAL* 1.3 57.5 - - - +
64C THR* 3.2 9.7 - - - +
65C ALA* 2.9 28.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il